Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers

dc.contributor.authorWienk, Raven
dc.contributor.authorMostert-O'Neill, Marja Mirjam
dc.contributor.authorAbeysekara, Nilwala
dc.contributor.authorManosalva, Patricia
dc.contributor.authorFreeman, Barbie
dc.contributor.authorVan den Berg, Noelani
dc.contributor.emailraven.wienk@up.ac.zaen_US
dc.date.accessioned2023-01-30T08:44:14Z
dc.date.issued2022-11
dc.descriptionDATA AVAILABILTY : The cultivar germplasm analysed during this study is available in the University of Pretoria Research Repository [Supple- mentary File 1—https://doi.org/10.25403/UPresearchdata.19145087]en_US
dc.descriptionSUPPLEMENTARY FILE 1 : Supplementary Fig 1 DAPC analysis of 159 genotypes indicating the cluster’s composition from K = 2 until K = 7 a) Bayesian information criterion (BIC) plot b) DAPC scatterplot - The eigenvalues and variance of each PC are found within parentheses on each axis. Individuals are represented as dots c) Genomic composition plot - Each thin vertical line in the bar plot represents one individual and each colour represents one inferred ancestral population. The length of each colour in a vertical bar represents the proportion of that individual’s ancestry that is derived from the inferred ancestral population corresponding to that colour. The same colour in different individuals indicates that they belong to the same cluster, indicating admixture (PDF 3451 KB)en_US
dc.descriptionSUPPLEMENTARY FILE 2 : Supplementary File 1: Formatted data of 326 genotyped individuals - Including industry suspected variety, DAPC assigned variety, assigned affinity propagation groups, silhouette scores, and genotype data (10.25403/UPresearchdata.19145087) (XLSX 663 KB)en_US
dc.description.abstractSince the start of avocado cultivation in South Africa, superior rootstocks and fruit cultivars have been selected based on morphological traits, which is time consuming and expensive. Technological advances, such as the development of a single nucleotide polymorphism (SNP) genotyping platform for avocado, may reduce these limitations. Therefore, the aim of this study was to implement molecular marker technologies for the validation of clonal material, verification of horticultural varieties, and determining the genetic diversity and population structure of an avocado cultivar germplasm in South Africa. An avocado cultivar breeding population, containing 375 individuals, was genotyped using 384 SNP markers. Our affinity propagation analysis (APA) indicated a 10.74% mislabelling in the germplasm. The principal component analysis (PCA) and discriminate analysis of principal components (DAPC) suggested that the germplasm was admixed in relation to the three known avocado varieties, Guatemalan, Mexican, and West Indian. Additionally, the ancestral origins were determined for 27 individuals with unknown ancestry. Furthermore, the population diversity was assessed and revealed moderate levels of differentiation in the germplasm, suggesting a high level of gene flow between the different populations. This research highlights the value of clonal verification and horticultural variety identification—for the reliable propagation of material with desired traits. The accurate propagation of material and clonal identity could aid avocado growers to link morphological characters and stress tolerance to accurate genetic backgrounds, which could improve the selection of avocados for current and future environmental stressors, especially as Africa is set to be significantly impacted by climate change.en_US
dc.description.departmentBiochemistryen_US
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.embargo2023-11-02
dc.description.librarianhj2023en_US
dc.description.sponsorshipThe Hans Merensky Foundation© and Allesbeste™.en_US
dc.description.urihttps://link.springer.com/journal/11295en_US
dc.identifier.citationWienk, R., Mostert-O’Neill, M., Abeysekara, N. et al. Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers. Tree Genetics & Genomes 18, 41 (2022). https://doi.org/10.1007/s11295-022-01573-8.en_US
dc.identifier.issn1614-2942 (print)
dc.identifier.issn1614-2950 (online)
dc.identifier.other10.1007/s11295-022-01573-8
dc.identifier.urihttps://repository.up.ac.za/handle/2263/89016
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.rights© 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature 2022. The original publication is available at : http://link.springer.comjournal/11295.en_US
dc.subjectPrincipal component analysis (PCA)en_US
dc.subjectDiscriminate analysis of principal components (DAPC)en_US
dc.subjectAvocadoesen_US
dc.subjectAvocado (Persea americana)en_US
dc.subjectSingle nucleotide polymorphism (SNP)en_US
dc.subjectPopulation structureen_US
dc.subjectGenetic admixtureen_US
dc.subjectBreedingen_US
dc.titleGenetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markersen_US
dc.typePostprint Articleen_US

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